There are about 895 species of vascular plant native to the islands of Sao Tomé and Principe, 95 of which are restricted to São Tomé and 37 that occur only on Príncipe. The families Orchidaceae, Rubiaceae and Euphorbiaceae are well represented, as are the genera Calvoa and Begonia. The giant endemic begonias Begonia crateris and Begonia baccata can reach three metres in height. The islands are also rich in ferns. The only gymnosperm is a single endemic species from São Tomé, Podocarpus mannii.

Rainforest covers about 74% of the country. Much of this is secondary forest that has grown on abandoned plantations. A large area of forest is protected by Obo National Park. Other habitats include savanna and mangroves.